The practice of injecting waste underground arose as a solution to an environmental crisis.

In the first half of the 20th century, toxic waste collected in cesspools, or was dumped in rivers or poured onto fields. As the consequences of unbridled pollution became unacceptable, the country turned to an out-of-sight alternative. Drawing on techniques developed by the oil and gas industry, companies started pumping waste back into wells drilled for resources. Toxic waste became all but invisible. Air and water began to get cleaner.

Then a host of unanticipated problems began to arise.

In April, 1967 pesticide waste injected by a chemical plant at Denver's Rocky Mountain Arsenal destabilized a seismic fault, causing a magnitude 5.0 earthquake -- strong enough to shatter windows and close schools -- and jolting scientists with newfound risks of injection, according to the U.S. Geological Survey.

A year later, a corroded hazardous waste well for pulping liquor at the Hammermill Paper Co., in Erie, Pa., ruptured. Five miles away, according to an EPA report, "a noxious black liquid seeped from an abandoned gas well" in Presque Isle State Park.

In 1975 in Beaumont, Texas, dioxin and a highly acidic herbicide injected underground by the Velsicol Chemical Corp. burned a hole through its well casing, sending as much as five million gallons of the waste into a nearby drinking water aquifer.

Then in August 1984 in Oak Ridge, Tenn., radioactive waste was turned up by water monitoring near a deep injection well at a government nuclear facility.

Regulators raced to catch up. In 1974, the Safe Drinking Water Act was passed, establishing a framework for regulating injection. Then, in 1980, the EPA set up the tiered classes of wells and began to establish basic construction standards and inspection schedules. The EPA licensed some state agencies to monitor wells within their borders and handled oversight jointly with others, but all had to meet the baseline requirements of the federal Underground Injection Control program.

Even with stricter regulations in place, 17 states – including Alabama, North Carolina, South Carolina and Wisconsin -- banned Class 1 hazardous deep well injection.

"We just felt like based on the knowledge that we had at that time that it was not something that was really in the best interest of the environment or the state," said James Warr, who headed Alabama's Department of Environmental Management at the time.

Injection accidents kept cropping up.

A 1987 General Accountability Office review put the total number of cases in which waste had migrated from Class 1 hazardous waste wells into underground aquifers at 10 -- including the Texas and Pennsylvania sites. Two of those aquifers were considered potential drinking water sources.

In 1989, the GAO reported 23 more cases in seven states where oil and gas injection wells had failed and polluted aquifers. New regulations had done little to prevent the problems, the report said, largely because most of the wells involved had been grandfathered in and had not had to comply with key aspects of the rules.

Noting four more suspected cases, the report also suggested there could be more well failures, and more widespread pollution, beyond the cases identified. "The full extent to which injected brines have contaminated underground sources of drinking water is unknown," it stated.

The GAO concluded that most of the contaminated aquifers could not be reclaimed because fixing the damage was "too costly" or "technically infeasible."

Faced with such findings, the federal government drafted more rules aimed at strengthening the injection program. The government outlawed certain types of wells above or near drinking water aquifers, mandating that most industrial waste be injected deeper.

The agency also began to hold companies that disposed of hazardous industrial waste to far stiffer standards. To get permits to dispose of hazardous waster after 1988, companies had to prove – using complex models and geological studies -- that the stuff they injected wouldn't migrate anywhere near water supplies for 10,000 years. They were already required to test for fault zones and to conduct reviews to ensure there were no conduits for leakage, such as abandoned wells, within a quarter-mile radius. Later, that became a two-mile minimum radius for some wells.

The added regulations would have prevented the vast majority of the accidents that occurred before the late 1980s, EPA officials contend.

"The requirements weren't as rigorous, the testing wasn't as rigorous and in some cases the shallow aquifers were contaminated," Kobelski said. "The program is not the same as it was when we first started."

Today's injection program, however, faces a new set of problems.

As federal regulators toughened rules for injecting hazardous waste, oil and gas companies argued that the new standards could drive them out of business. State oil and gas regulators pushed back against the regulations, too, saying that enforcing the rules for Class 2 wells – which handle the vast majority of injected waste by volume -- would be expensive and difficult.

Ultimately, the energy industry won a critical change in the federal government's legal definition of waste: Since 1988, all material resulting from the oil and gas drilling process is considered non-hazardous, regardless of its content or toxicity.

"It took a lot of talking to sell the EPA on that and there are still a lot of people that don't like it," said Bill Bryson, a geologist and former head of the Kansas Corporation Commission's Conservation Division, who lobbied for and helped draft the federal rules. "But it seemed the best way to protect the environment and to stop everybody from just having to test everything all the time."

The new approach removed many of the constraints on the oil and gas industry. They were no longer required to conduct seismic tests (a stricture that remained in place for Class 1 wells). Operators were allowed to test their wells less frequently for mechanical integrity and the area they had to check for abandoned wells was kept to a minimum – one reason drilling waste kept bubbling to the surface near Chico.

Soon after the first Chico incident, Texas expanded the area regulators were required to check for abandoned waste wells (a rule that applied only to certain parts of the state). Doubling the radius they reviewed in Chico to a half mile, they found 13 other injection or oil and gas wells. When they studied the land within a mile – the radius required for review of many Class 1 wells – officials discovered another 35 wells, many dating to the 1950s.

The Railroad Commission concluded that the Chico injection well had overflowed: The target rock zone could no longer handle the volume being pushed into it. Trying to cram in more waste at the same speed could cause further leaks, regulators feared. The commission set new limits on how fast the waste could be injected, but did not forbid further disposal. The well remains in use to this day.

In late 2008, samples of Chico's municipal drinking water were found to contain radium, a radioactive derivative of uranium and a common attribute of drilling waste. The water well was a few miles away from the leaking injection well site, but environmental officials said the contaminants discovered in the water well were unrelated, mostly because they didn't include the level of sodium typical of brine.

Since then, Ed Cowley, the public works director, said commission officials have continued to assure him that brine won't reach Chico's drinking water. But since the agency keeps allowing more injection and doesn't track the cumulative volume of waste going into wells in the area, he's skeptical that they can keep their promise.

"I was kind of like, ‘You all need to get together and look at the total amount you are trying to fit through the eye of the needle,'" he said.

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When sewage flowed from 20 Class 1 wells near Miami into the Upper Floridan aquifer, it challenged some of scientists' fundamental assumptions about the injection system.

The wells – which had helped fuel the growth of South Florida by eliminating the need for expensive water treatment plants -- had passed rigorous EPA and state evaluation throughout the 1980s and 1990s. Inspections showed they were structurally sound. As Class 1 wells, they were subject to some of the most frequent tests and closest scrutiny.

Yet they failed.

The wells' designers would have calculated what is typically called the "zone of influence" — the space that waste injected into the wells was expected to fill. This was based on estimates of how much fluid would be injected and under what pressure.

In drawings, the zone of influence typically looks like a Hershey's kiss, an evenly dispersed plume spreading in a predictable circular fashion away from the bottom of the well. Above the zone, most drawings depict uniform formations of rock not unlike a layer cake.

Based on modeling and analysis by some of the most sophisticated engineering consultants in the country, Florida officials, with the EPA's assent, concluded that waste injected into the Miami-area wells would be forever trapped far below the South Florida peninsula.

"All of the modeling indicated that the injectate would be confined in the injection zone," an EPA spokesperson wrote to ProPublica in a statement.

But as Miami poured nearly half a billion gallons of partly treated sewage into the ground each day from the late 1980s through the mid 1990s, hydrogeologists learned that the earth – and the flow of fluids through it – wasn't as uniform as the models depicted. Florida's injection wells, for example, had been drilled into rock that was far more porous and fractured than scientists previously understood.

"Geology is never what you think it is," said Ronald Reese, a geologist with the United States Geological Survey in Florida who has studied the well failures there. "There are always surprises."

Other gaps have emerged between theories of how underground injection should work and how it actually does. Rock layers aren't always neatly stacked as they appear in engineers' sketches. They often fold and twist over on themselves. Waste injected into such formations is more likely to spread in lopsided, unpredictable ways than in a uniform cone. It is also likely to channel through spaces in the rock as pressure forces it along the weakest lines.

Petroleum engineers in Texas have found that when they pump fluid into one end of an oil reservoir to push oil out the other, the injected fluid sometimes flows around the reservoir, completely missing the targeted zone.

"People are still surprised at the route that the injectate is taking or the bypassing that can happen," said Jean-Philippe Nicot, a research scientist at the University of Texas' Bureau of Economic Geology.

Conventional wisdom says fluids injected underground should spread at a rate of several inches or less each year, and go only as far as they are pushed by the pressure inside the well. In some instances, however, fluids have travelled faster and farther than researchers thought possible.

In a 2000 case that wasn't caused by injection but brought important lessons about how fluids could move underground, hydrogeologists concluded that bacteria-polluted water migrated horizontally underground for several thousand feet in just 26 hours, contaminating a drinking water well in Walkerton, Ontario, and sickening thousands of residents. The fluids travelled 80 times as fast as the standard software model predicted was possible.

According to the model, vertical movement of underground fluids shouldn't be possible at all, or should happen over what scientists call "geologic time": thousands of years or longer. Yet a 2011 study in Wisconsin found that human viruses had managed to infiltrate deep aquifers, probably moving downward through layers believed to be a permanent seal.

According to a study published in April in the journal Ground Water, it's not a matter of if fluid will move through rock layers, but when.

Tom Myers, a hydrologist, drew on research showing that natural faults and fractures are more prevalent than commonly understood to create a model that predicts how chemicals might move in the Marcellus Shale, a dense layer of rock that has been called impermeable. The Marcellus Shale, which stretches from New York to Tennessee, is the focus of intense debate because of concerns that chemicals injected in drilling for natural gas will pollute water.

Myers' new model said that chemicals could leak through natural cracks into aquifers tapped for drinking water in about 100 years, far more quickly than had been thought. In areas where there is hydraulic fracturing or drilling, Myers' model shows, man-made faults and natural ones could intersect and chemicals could migrate to the surface in as little as "a few years, or less."

"It's out of sight, out of mind now. But 50 years from now?" Myers said, referring to injected waste and the rock layers trusted to entrap it. "Simply put, they are not impermeable."

Myers' work is among the few studies done over the past few decades to compare theories of hydrogeology to what actually happens. But even his research is based on models.

"A lot of the concepts and a lot of the regulations that govern this whole practice of subsurface injection is kind of dated at this point," said one senior EPA hydrologist who was not authorized to speak to ProPublica, and declined to be quoted by name.

"It's a problem," he said. "There needs to be a hard look at this in a new way."